I am contributing here as a broker for liveaboard bookings all over SE Asia.
My company is Thailand-registered, and when I book a Thailand liveaboard for my clients, I can take credit cards, but when I book a trip in another country, I have to ask for wire transfers. Furthermore, I have to send wire transfers to boat operators in those countries.
Why? In the vast majority of cases, boat operators do not have credit card facilities, and the ones that do accept credit cards often have off-site payment locations not related to the area where their boats sail--that is, a boat may sail in Indonesia (or Thailand or Maldives or the Philippines) and yet require payment--regardless of whether by credit card or wire transfer--to the UK, Hong Kong, the US or elsewhere. It's very common among operators that accept credit card payments.
You may also wonder why I can take credit cards for Thailand and not for other countries--my credit card facility only accepts Thai baht payment, so there are all kinds of issues related to that, ranging from multiple currency exchanges and commissions on them to invoicing and receipts for audits, etc. I just can't take credit cards for non-Thailand bookings.
Finally, in Indonesia the banking laws changed a few years ago and only allow hotels to accept credit cards that are not presented on the spot, with the card inserted into the actual land-based machine. This means that any operator or agent that has an Indonesia-based payment location can only take wire transfers or Western Union or Pay Pal or the like. There is no actual bank-to-bank option other than a wire transfer.
In sum:
1) It's usual for liveaboard operators and agents based in SE Asia to request wire transfers.
2) When sending money to a third country, you will most often have to do a TT (wire) transfer unless the operator has a branch of its business registered in that country and can get a credit card merchant number there. Such liveaboard businesses are the exception rather than the rule, and they are almost always the priciest ones.
3) It doesn't matter if you're working directly with the operator or an agent in regard to payment options; what matters is where the business is registered. Different countries have different banking and credit card regulations.
4) Agents based in countries like the UK and the US have a very limited view of liveaboard operators/boats and typically don't recommend some very good options simply out of ignorance--they aren't here and they don't know the lay of the land like regionally-based agents do.